.. _gmx do_dssp:

gmx do_dssp
===========

Synopsis
--------

.. parsed-literal::

    gmx do_dssp [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                [:strong:`-map` :emphasis:`[<.map>]`] [:strong:`-ssdump` :emphasis:`[<.dat>]`] [:strong:`-o` :emphasis:`[<.xpm>]`]
                [:strong:`-sc` :emphasis:`[<.xvg>]`] [:strong:`-a` :emphasis:`[<.xpm>]`] [:strong:`-ta` :emphasis:`[<.xvg>]`]
                [:strong:`-aa` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
                [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-sss` :emphasis:`<string>`]
                [:strong:`-ver` :emphasis:`<int>`]

Description
-----------

``gmx do_dssp``
reads a trajectory file and computes the secondary structure for
each time frame
calling the dssp program. If you do not have the dssp program,
get it from https://swift.cmbi.umcn.nl/gv/dssp. ``gmx do_dssp`` assumes
that the dssp executable is located in
``/usr/local/bin/dssp``. If this is not the case, then you should
set an environment variable ``DSSP`` pointing to the dssp
executable, e.g.:

``setenv DSSP /opt/dssp/bin/dssp``

The dssp program is invoked with a syntax that differs
depending on version. Version 1, 2 and 4 are supported, and the correct
invocation format can be selected using the ``-ver`` option.
By default, do_dssp uses the syntax introduced with version 2.0.0.
Newer versions might also have executable name ``mkdssp`` instead
of ``dssp``.

The structure assignment for each residue and time is written to an
:ref:`.xpm <xpm>` matrix file. This file can be visualized with for instance
``xv`` and can be converted to postscript with ``xpm2ps``.
Individual chains are separated by light grey lines in the :ref:`.xpm <xpm>` and
postscript files.
The number of residues with each secondary structure type and the
total secondary structure (``-sss``) count as a function of
time are also written to file (``-sc``).

Solvent accessible surface (SAS) per residue can be calculated, both in
absolute values (A^2) and in fractions of the maximal accessible
surface of a residue. The maximal accessible surface is defined as
the accessible surface of a residue in a chain of glycines.
**Note** that the program [gmx-sas] can also compute SAS
and that is more efficient.

Finally, this program can dump the secondary structure in a special file
``ssdump.dat`` for usage in the program :doc:`gmx chi <gmx-chi>`. Together
these two programs can be used to analyze dihedral properties as a
function of secondary structure type.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file
``-map`` [<.map>] (ss.map) (Library)
    File that maps matrix data to colors

Options to specify output files:

``-ssdump`` [<.dat>] (ssdump.dat) (Optional)
    Generic data file
``-o`` [<.xpm>] (ss.xpm)
    X PixMap compatible matrix file
``-sc`` [<.xvg>] (scount.xvg)
    xvgr/xmgr file
``-a`` [<.xpm>] (area.xpm) (Optional)
    X PixMap compatible matrix file
``-ta`` [<.xvg>] (totarea.xvg) (Optional)
    xvgr/xmgr file
``-aa`` [<.xvg>] (averarea.xvg) (Optional)
    xvgr/xmgr file

Other options:

``-b`` <time> (0)
    Time of first frame to read from trajectory (default unit ps)
``-e`` <time> (0)
    Time of last frame to read from trajectory (default unit ps)
``-dt`` <time> (0)
    Only use frame when t MOD dt = first time (default unit ps)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-[no]w``  (no)
    View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <pdb>` files
``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-sss`` <string> (HEBT)
    Secondary structures for structure count
``-ver`` <int> (2)
    DSSP major version. Syntax changed with version 2 and 4.

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

   More information about |Gromacs| is available at <http://www.gromacs.org/>.